Pro-biomics: Omics Technologies To Unravel the Role of Probiotics in Health and Disease

Abstract

The comprehensive characterization of probiotic action has flourished during the past few decades, alongside the evolution of high-throughput, multiomics platforms. The integration of these platforms into probiotic animal and human studies has provided valuable insights into the holistic effects of probiotic supplementation on intestinal and extraintestinal diseases. Indeed, these methodologies have informed about global molecular changes induced in the host and residing commensals at multiple levels, providing a bulk of metagenomic, transcriptomic, proteomic, and metabolomic data. The meaningful interpretation of generated data remains a challenge; however, the maturation of the field of systems biology and artificial intelligence has supported analysis of results. In this review article, we present current literature on the use of multiomics approaches in probiotic studies, we discuss current trends in probiotic research, and examine the possibility of tailor-made probiotic supplementation. Lastly, we delve deeper into newer technologies that have been developed in the last few years, such as single-cell multiomics analyses, and provide future directions for the maximization of probiotic efficacy.

Whole-Genome Sequencing, Phylogenetic and Genomic Analysis of Lactiplantibacillus pentosus L33, a Potential Probiotic Strain Isolated From Fermented Sausages

“…The proposed health effects of new isolates should be thoroughly explored in vitro and in vivo , to finally be validated in the clinical setting ( FAO/WHO, 2002 ). Mechanistic studies on host-probiotic interactions have flourished recently, with the advent of multi-omics technologies, facilitating a better understanding of their properties and biological functions ( Kiousi et al, 2021 ).…”

The Clash of Microbiomes: From the Food Matrix to the Host Gut

“…On the other hand, even mild changes in the structure of the microbiome can have an amplified effect on its metabolic function. One consequence that has been documented across several studies is that probiotics can enhance the populations of SCFA producers, leading to changes in the metabolic profile of the microbiome [46]. SCFAs have been linked with various physiological effects, such as immunomodulatory actions [47], and thus they can act as 'messengers' of changes in the gut microbiome that can systemically affect the host.…”

“…As such, the main advantage of using these platforms is that they can provide a global snapshot of the expression of human cells after microbial stimuli. The meaningful interpretation of the extracted data can result in the construction of networks to map probiotic effects on the host [46]. Furthermore, these global, unbiased approaches can reveal unexpected results and generate new leads for microbe-host interactions.…”

Evaluating the Role of Probiotics in the Prevention and Management of Age-Related Diseases

“…Only a subgroup of lactobacilli can be termed as probiotics, that present confirmed health-promoting properties, such as anti-inflammatory, immunomodulatory [ 146 ], antibacterial, antibiofilm [ 147 ] actions, contrary to common misconceptions. The increased use of omics platforms to study the biology of probiotic microorganisms at multiple levels, as well as host response can reveal their mechanisms of action and provide a basis for targeted interventions [ 148 ]. More specifically, profiling the metabolic capacity of the strains and the production and secretion of bioactive compounds has shed light on their biological potential.…”